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Best practices for variant calling in clinical sequencing
- Source :
- Genome Medicine, Vol 12, Iss 1, Pp 1-13 (2020), Genome Medicine
- Publication Year :
- 2020
- Publisher :
- Springer Science and Business Media LLC, 2020.
-
Abstract
- Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as cancer. Accurate variant calling in NGS data is a critical step upon which virtually all downstream analysis and interpretation processes rely. Just as NGS technologies have evolved considerably over the past 10 years, so too have the software tools and approaches for detecting sequence variants in clinical samples. In this review, I discuss the current best practices for variant calling in clinical sequencing studies, with a particular emphasis on trio sequencing for inherited disorders and somatic mutation detection in cancer patients. I describe the relative strengths and weaknesses of panel, exome, and whole-genome sequencing for variant detection. Recommended tools and strategies for calling variants of different classes are also provided, along with guidance on variant review, validation, and benchmarking to ensure optimal performance. Although NGS technologies are continually evolving, and new capabilities (such as long-read single-molecule sequencing) are emerging, the “best practice” principles in this review should be relevant to clinical variant calling in the long term.
- Subjects :
- Best practices
DNA Copy Number Variations
lcsh:QH426-470
Computer science
Systems biology
Best practice
Clinical Decision-Making
DNA Mutational Analysis
lcsh:Medicine
Review
Computational biology
DNA sequencing
Variant calling
Genetics
Clinical genetic
Humans
Mutation detection
Genetic Testing
Clinical sequencing
Molecular Biology
Exome
Germ-Line Mutation
Cancer sequencing
Genetics (clinical)
lcsh:R
Computational Biology
Disease Management
Genetic Variation
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Benchmarking
Human genetics
lcsh:Genetics
Molecular Diagnostic Techniques
Mutation
Next-generation sequencing
Molecular Medicine
Subjects
Details
- ISSN :
- 1756994X
- Volume :
- 12
- Database :
- OpenAIRE
- Journal :
- Genome Medicine
- Accession number :
- edsair.doi.dedup.....5b841280bc0430341082df9fd5f77585